Difference between revisions of "Load Genome Script"
From CoGepedia
(Created page with 'The load genome script, load_genome.pl, allows genomes to be created via the backend. Usage: <pre> perl load_genome.pl -name <string> -desc <string> ... </pre> Required paramet...') |
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Required parameters: | Required parameters: | ||
| − | fasta_files | + | <pre> |
| − | staging_dir | + | fasta_files comma-separated list of FASTA files |
| − | install_dir | + | staging_dir temporary staging directory for processing files, use "." |
| − | user_id | + | install_dir permanent installation directory for genome files with DATADIR in configuration file |
| − | config | + | user_id user ID |
| + | config configuration file | ||
| + | </pre> | ||
Optional parameters: | Optional parameters: | ||
| − | name | + | <pre> |
| − | desc | + | name String name of the genome |
| − | link | + | desc String description of the genome |
| − | version | + | link URL to the data source or publication |
| − | type_id | + | version Version of the genome data |
| − | restricted | + | type_id Sequence type ID, defaults to 1 for "unmasked" |
| − | organism_id | + | restricted Flag to make genome private (1) or public (0) |
| − | source_name | + | organism_id Organism ID |
| − | source_desc | + | source_name Name of data source, e.g. the lab that generated the sequence data |
| + | source_desc Description of the data source | ||
| + | </pre> | ||
Revision as of 10:30, 16 February 2015
The load genome script, load_genome.pl, allows genomes to be created via the backend.
Usage:
perl load_genome.pl -name <string> -desc <string> ...
Required parameters:
fasta_files comma-separated list of FASTA files staging_dir temporary staging directory for processing files, use "." install_dir permanent installation directory for genome files with DATADIR in configuration file user_id user ID config configuration file
Optional parameters:
name String name of the genome desc String description of the genome link URL to the data source or publication version Version of the genome data type_id Sequence type ID, defaults to 1 for "unmasked" restricted Flag to make genome private (1) or public (0) organism_id Organism ID source_name Name of data source, e.g. the lab that generated the sequence data source_desc Description of the data source
